R'lyeh is seen to rise when the stars are right; however, it is located "closer than Communist Cuba" off the Californian coast, not in its usual location in the South Pacific, however, this may be due to the twisted geometry mentioned below.

Cassidy mentions the Three-Lobed Burning Eye and the "Al-Azif" to Kerouac in predicting the coming apocalypse. Kerouac later states that he sent Cthulhu back to "strange aeons," another reference to the Necronomicon.

Shoggoths appear several times; however, instead of how they are usually depicted in the Mythos, they appear as agents of Cthulhu that assume the shapes, forms, or personal appearances most likely to drive their target mad.

Kerouac talks about trying to get the government to send the "Sea Hunt and gut the Elder God," a possible reference to the submarine torpedoing of Y'ha-nthlei at the beginning/end of "The Shadow Over Innsmouth."

A reference is made to Lovecraft himself; a worker mentions how a serious "gentleman from Providence" named Mr. Love passed through several weeks earlier, predicting the onslaught and building a lighthouse in the desert. He is described as having "eyes so round like a frog's [with a] lipless mouth," characteristics matching the "Innsmouth Look" of the Deep Ones.

Kerouac observes Azathoth in the twisted constellations. Cassady later becomes an avatar for Azathoth.

After Cthulhu comes to power, all money must be stamped with the Elder Sign; both Lovecraft's branching symbol and August Derleth's five-pointed flaming star variants are mentioned. This could be a reference to the Mark of the Beast being needed for commerce.

Chicago is described as being formed of "Cyclopean modern towers and pinnacles rising flowerlike and delicate like spun crystal"; this is similar to Lovecraft's description of R'lyeh, Pnakotus, and the City of the Old Ones.

The established religions all begin preaching to Cthulhu rather than the Christian god; they are referred to as "cargo cults" and Kerouac uses the term "starry wisdom" to describe them. These are references to several Cthulhu Mythos cults, specifically the Church of Starry Wisdom and the Esoteric Order of Dagon.

The limited edition hardcover includes the short story "Jitterbuggin'", an afterword, a bound-in ribbon bookmark, and a unique Lovecraftian senryū written by Mamatas. 100 copies of the limited edition were produced, and the senryū were collected as Cthulhu Senryū (Prime Books, 2006)

Positive word of mouth continued long after the releases of the hardcover and paperback releases. As recently as 2009, major genre publications such as Tor.com published an article on the book [2] by novelist Jon Evans. In September 2010, Kenneth Hite declared the book one of the best Cthulhu Mythos stories not written by Lovecraft, in his book Cthulhu 101. Hite also declared the book one of the top five Mythos novels of all time via Twitter.[3] In an October 2010 podcast and interview,[4] author Nick Mamatas explained that his goal in writing Move Under Ground was to write a novel that would still be discussed ten years after its initial publication, referencing The Enemies of Promise by Cyril Connolly.